Biostar Tidyr

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dplyr tidyr

updated 2.5 years ago by Martin Morgan 25k • written 2.5 years ago by Marco Blanchette ▴ 30

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Rscript tidyr dataframe tidyverse offtopic

updated 5 months ago by Marcel Ramos 620 • written 6 months ago by Nikhil • 0

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Answer: batch effect correction before DESeq2 analysis by ATpoint ★ 2.1k

This is covered in the vignette. Including batch into the design is recommending for DE testing and removal from transformed counts is reco…

Answer: Reproducibility using limma for DE Analysis by TSauer • 0

Yes, i know that. However, I implemented the imputation step quite long ago, using a different package, exported the data and then did the …

Comment: Reproducibility using limma for DE Analysis by Gordon Smyth 47k

limma can also be run without imputation, i.e., leaving the missing values as NA.

Comment: Reproducibility using limma for DE Analysis by TSauer • 0

Hey Gordon, thank you for the swift response. Indeed, I do perform imputation. Weirdly, it did not occur to me that this could be the origi…

Answer: Reproducibility using limma for DE Analysis by Gordon Smyth 47k

limma has no random component and limma analyses are completely reproducible. limma doesn't have any dependence on the random number seed. …

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Answer: Reproducibility using limma for DE Analysis

A: Can't load package "org.Hs.eg.db"

A: edgeR: exactTest, glmFIt or glmQLFit approach?

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